During the war, in 1942, Karajan married Anita Gütermann. She was the daughter of a rich man who had a business making sewing machines. His wife was partly Jewish. This caused the Nazi’s to talk about whether Karajan should still be allowed to conduct. By 1944, he was not in favour with the Nazis, but he was still conducting in Berlin. He left Berlin and went to Milan, Italy with his wife in February 1945. Karajan divorced Anita in 1958.

Although he was deposed after the war because of his Nazi connections, he started to conduct again in 1946.

He very often conducted the Vienna Philharmonic and gave many concerts at the Salzburg Festival. He continued to work very hard performing, conducting, and recording until his death in 1989. In Karajan's last years he left the Berlin Philharmonic after arguments with them, and concentrated on working again with the Vienna State Opera and the Vienna Philharmonic.

Herbert von Karajan had very good musicianship and memory. He conducted without a score in front of him, very often with his eyes closed. He is remembered for being very strict (like a dictator) and always insisting on having things the way he wanted. There are many stories about him that show this. He insisted on being paid very high fees. When he was being filmed conducting an orchestra, he wanted the cameras to show him all the time. When he conducted Wagner at the Metropolitan Opera, he made the stand for the conductor higher so that the audience could see him.